Rainwater then chose to undertake postgraduate studies at Columbia University. At the time this was an unusual move for a scholar from California, as Columbia was not then renowned for its physics; but this had recently changed. George B. Pegram had recently built up the physics department, and hired Scientists like Enrico Fermi. At Columbia Rainwater studied under Isidor Isaac Rabi, Enrico Fermi, Edward Teller and John R. Dunning. Fermi was engaged in neutron moderator studies that would lead to the construction of the first nuclear reactor, while Dunning and Eugene T. Booth had built Columbia's first cyclotron, in the basement of the Pupin Physics Laboratories. Rainwater received his Master of Arts in 1941. For his Doctor of Philosophy thesis on "Neutron beam spectrometer studies of boron, cadmium, and the Energy distribution from paraffin", written under Dunning's supervision, he built a neutron spectrometer and developed techniques for its use. Rainwater married Emma Louise Smith in March 1942. They had three sons, James, Robert and william and a daughter, Elizabeth Ann, who died from leukaemia when she was nine.